RetrogeneDB ID: retro_ocun_1547

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: AAGW02083491:2046..2888(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: UHMK1
• Ensembl ID: ENSOCUG00000012411
• Aliases: None
• Description: U2AF homology motif (UHM) kinase 1 [Source:HGNC Symbol;Acc:19683]

Sequence

>retro_ocun_1547
TCCAGAGATGTTCTGGAAGGCCTTGCTCTCCTTCATCATGAGGGTCGTGTCCACGCAGACCTCAAACCACAGAACATACT
GTGGAGTGCAGAGAACGAATGTTTTAAACTCACTGACTTTGGACTTAGCTTCAAAGAAGGCACTCCGGGTGTAAAGTACA
TTCAAACAGACGGGTGTCGTGCTCCAGAAGCAGAGCTGAAAAATCACGTGGCCCAGGCTGGCCTGCAGAGTGATACATAA
TGTAGCTCGGCTGCTGGTCTGCGGAGCCTAGGAATCATTTTACTGGAAATGTTCTCAGGAACGAAGCTGAAGCATACAGT
CCGATCTCAGGAATGGAAGGCAAGCAGTTCTGCTGTTGTTGATGAGATATTTGCCGGTAAAGCAGTGGTGAATGCCACAA
TTCCAACCCGTCACCTAAGAGACCTTATCAAAAGCATGCTTCATGATGATCCAAGCTGAAGAGTTCCTGCTGAAATGGCA
TCACGCAGCCCATTCGTTAGCATTCCTTTTGCCCCTCATGTTGAAGATCTGATGGTAGTTCCTACCCCACTGCTAAGACT
GCTGAGCGTGCTAGATGATGATCATCTTGAGAATGAAGAGGAACATGAAGATATTGTAGAAGATGTAAAAGAGGAATGCC
AGAAATATGGACCCGTGATATCTCCGCTTGTCCAAAGGAAAATCCTGGCAGAGGGCAAGTCTTTGTCGAGTATGCCAATG
CTGGTGGTTCCAAAGACGCTCAGGAATTACTGACCGGAAGGATGTTTGATGGGAAGTTTGTCATGGCTACATTCTACCCG
CAGAGTGCCTACAAGAGGGGATATCTGTATCAAACCTTGCTT

Alignment

ORF - retro_ocun_1547 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.98 %
• Parental protein coverage: 67.06 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ARDVLEALAFLHHEGYVHADLKPRNILWSAENECFKLIDFGLSFKEGNQDVKYIQTDGYRAPEAELQNCL
          .RDVLE.LA.LHHEG.VHADLKP.NILWSAENECFKL.DFGLSFKEG...VKYIQTDG.RAPEAEL.N..
Retrocopy SRDVLEGLALLHHEGRVHADLKPQNILWSAENECFKLTDFGLSFKEGTPGVKYIQTDGCRAPEAELKNHV

Parental  AQAGLQSDTECTSAVDLWSLGIILLEMFSGMKLKHTVRSQEWKANSSAIIDHIFASKAVVNAAIPAYHLR
          AQAGLQSDT.C.SA..L.SLGIILLEMFSG.KLKHTVRSQEWKA.SSA..D.IFA.KAVVNA.IP..HLR
Retrocopy AQAGLQSDT*CSSAAGLRSLGIILLEMFSGTKLKHTVRSQEWKASSSAVVDEIFAGKAVVNATIPTRHLR

Parental  DLIKSMLHDDPSRRIPAEMALCSPFFSIPFAPHIEDLVMLPTPVLRLLNVLDDDYLENEEEYEDIVEDVK
          DLIKSMLHDDPS.R.PAEMA..SPF.SIPFAPH.EDL...PTP.LRLL.VLDDD.LENEEE.EDIVEDVK
Retrocopy DLIKSMLHDDPS*RVPAEMASRSPFVSIPFAPHVEDLMVVPTPLLRLLSVLDDDHLENEEEHEDIVEDVK

Parental  EECQKYGPVVSLLV-PKENPGRGQVFVEYANAGDSKAAQKLLTGRMFDGKFVVATFYPLSAYKRGYLYQT
          EECQKYGPV.S.LV.PKENPGRGQVFVEYANAG.SK.AQ.LLTGRMFDGKFV.ATFYP.SAYKRGYLYQT
Retrocopy EECQKYGPVISPLV<PKENPGRGQVFVEYANAGGSKDAQELLTGRMFDGKFVMATFYPQSAYKRGYLYQT

Parental  LL
          LL
Retrocopy LL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.11 RPM	6.79 RPM
SRP017611_kidney	0.61 RPM	5.37 RPM
SRP017611_liver	0.00 RPM	2.77 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1547 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1547 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1547 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000001048	1 retrocopy	retro_mdom_103,
Oryctolagus cuniculus	ENSOCUG00000012411	3 retrocopies	retro_ocun_1245, retro_ocun_1535, retro_ocun_1547 ,
Rattus norvegicus	ENSRNOG00000002941	1 retrocopy	retro_rnor_1274,